He continued to feature regularly for Werder, although he struggled with injuries in his later years. Baumann scored the goal that took Bremen to the 2009 UEFA Cup Final, in the second leg of the semifinal against Hamburger SV, from a corner conceded by after the ball had deflected off a crumpled up piece of paper thrown from the home supporters. He announced his retirement on 20 May 2009,[2] as his contract was to expire the following month.[3]

In May 2009, Baumann became the club's assistant general manager, joining another former player, Klaus Allofs, in his staff. At the end of the 2014–15 season, he left his position as "director of first-team football and scouting" after 2½ years.[4][5]

Baumann featured in 28 internationals, scoring two goals.[6] His debut for Germany came in a 1–0 victory against Norway in Oslo, on 14 November 1999, becoming the 800th player to be capped by the German national team.[7]